Failure to close account and charging fees

My mother has had two loans with Clientele (Direct Axis) for a number of years. As she has been affected by current lock down, I have assisted her in settling both these amounts in full in order to alleviate her financial stress. A direct transfer on her FNB online banking profile was made to settle these loans on the 21 April 2020, she called Clientele and advised them to close the accounts and also sent them an email. I have checked her account every day and both amounts are reflecting positively. They have failed to close the accounts debited her on the 25 April 2020 and charged her additional fees even though the accounts are now in positive? She is 67 years old and has had to go into the municipality to obtain proof of residence just to close the accounts. I cannot believe how an institution would fail to assist a good paying customer that just wants to settle and close an account. Regardless she has had no one contact her to resolve this despite numerous emails and requests.